Average Shannon's Information Index Research Articles

Genetic Diversity and Construction of Core Collection of Sterculia Germplasm

Amplification of 107 Sterculia accessions with 12 ISSR primers resulted in 235 bands, the percentage of polymorphic sites was 100%, with the average number of effective alleles (Ne) of 1.2464, the average Nei’s gene diversity index (H) of 0.1556, the average Shannon's information index (I) of 0.2563, and the average polymorphism information content (PIC) of 0.8594, indicating that the collected 107 accessions had high genetic diversity. The genetic diversity was unevenly distributed among Sterculia samples collected from different provinces, and the highest value was observed in samples from Guangdong Province, followed by those from Yunnan Province, and the lowest was from Guangxi Province. The core collection construction of the 107 Sterculia accessions was carried out by using the SCR and LDSS methods, respectively, and the results showed that the LDSS method was more suitable for Sterculia germplasm. Different core collections were constructed based on sampling proportions of 35, 30, 25, 20 and 15%, respectively, the t-test and principal coordinates analysis results showed that the genetic diversity of the original germplasm can be fully represented at a sampling proportion of 30%. Bangladesh J. Bot. 53(2): 319-325, 2024 (June)

Genetic Diversity and Population Structure of the Invasive Oriental Fruit Fly, Bactrocera dorsalis (Diptera: Tephritidae) in Burkina Faso.

Bactrocera dorsalis Hendel is a highly invasive horticultural pest that is of major economic importance worldwide. In Burkina Faso, it is one of the main insect pests that affects the production and exportation of mangos. Understanding the biology and the genetic dynamics of this insect pest provides crucial information for the development of effective control measures. The aim of this study was to understand the distribution, diversity, and genetic structure of B. dorsalis in Burkina Faso. Male flies were collected transversally in Burkina Faso and analyzed by PCR using 10 microsatellite markers. The results showed an abundance of B. dorsalis varying from 87 to 2986 flies per trap per day at the different sampling sites. The genetic diversity was high at all sites, with an average Shannon's Information Index (I) of 0.72 per site. The gene flow was high between study populations and ranged from 10.62 to 27.53 migrants. Bayesian admixture analysis showed no evidence of structure, while Discriminant Analysis of Principal Components identified three weakly separated clusters in the population of B. dorsalis in Burkina Faso. The results of this study could be used to optimize the effectiveness of current control interventions and to guide the implementation of new, innovative, and sustainable strategies.

김해 야생차 군락지들의 차나무에 대한 유전적 다양성 분석

This study examined the genetic diversity of 13 tea tree samples to establish a variety discrimination system for the three Gimhae wild tea colonies using ISSR markers and to provide basic data for genetic diversity analysis. Seven primers that showed polymorphic and reproducible results among 100 ISSR universal primers were selected and used to amplify the genomic DNA of the 13 tea trees from three Gimhae wild tea colonies. The results demonstrated that all seven primers generated 117 bands with a 100% polymorphic band ratio. The average observed number of alleles was 2.0. The average effective number of alleles was 1.5323, while the average Nei's gene diversity was 0.3271. The average Shannon's Information index was 0.5001. The genetic similarity among the 13 tea tree samples ranged from 0.4444 to 0.8718, while the genetic distance ranged from 0.1372 to 0.8109. The 13 tea trees in three Gimhae wild colonies displayed a high level of genetic diversity, and the Dongsangdong and Sangdong samples in the three Gimhae wild colonies had a genetic similarity greater than 0.8 with Chinese tea species, indicating a close relationship with Chinese tea. Overall, these findings provide a theoretical basis for preserving and cultivating Gimhae wild tea trees.

EST-SSR development and genetic diversity in the medicinal plant Pseudostellaria heterophylla (Miq.) Pax

Pseudostellaria heterophylla is a perennial herb plant with high medicinal value. Germplasm development and improvement play a crucial role in the modern pseudostellaria industry. In present study, we genotyped 10 representative cultivars and 102 F1 hybrid individuals with developed markers in China, aiming at (1) screening a set of markers for correctly identifying P. heterophylla cultivars and F1 hybrid individuals, and (2) confirming the genetic diversity and parent-offspring (PO) relationships among them. The results showed that 360 EST-SSR markers were developed using transcriptome library. Based on genotyping data of 10 representative cultivars, 20 of them showed high fingerprinting power and genetic diversity with mean observed heterozygosity (Ho), Shannon's Information Index (I), PI and PIsibs value of 0.330, 0.560, 0.505 and 0.704, respectively. A combination of 20 markers could further reduce the value. of PI and PIsibs to 3.2 × 10−7 and 6.7 × 10−4, respectively. Furtherly, above 20 EST-SSR were recommended as a set marker for analyzing the genetic diversity and parentage of 102 F1 hybrid individuals. The results showed that the markers are highly polymorphic among the F1 individuals with an average Shannon's Information Index of 0.642. It was possible to discriminate 100 test samples by a combination of twenty markers, and the overall possibility of finding two random individuals having the same genotypes across the 20 loci was estimated to be 2.0 × 10−8. Meanwhile, parentage analysis based on the genotyping data confirmed 63 pairs of putative PO relationships, whereas the other 13 were identified as pseudo-hybrids relationships. Overall, this study will provide 20 credible EST-SSR marker and 102 hybrid materials for further germplasm conservation, genetic improvement, genetic mapping and functional gene location.

Construction and characterization of microsatellite markers for the Neptune whelk, Neptunea cumingii

The Neptune whelk, Neptunea cumingii, is an economic gastropod endemic to the East Asia Warm Temperate Biotic Subregion. The study of the development in microsatellite markers maybe beneficial for assessing the genetic diversity and conservation of resources on this dwindling species. The microsatellite markers were constructed and characterized through Illumina high-throughput sequencing and capillary electrophoresis techniques. Eleven polymorphic microsatellite loci were screened and validated. The observed heterozygosity and expected heterozygosity of each locus showed a range from 0.0600 to 0.6508 and from 0.7380 to 0.9375, respectively. The average Shannon's information index and polymorphism information content were 2.0828 and 0.8325, respectively. Deviation from all loci was generated from Hardy-Weinberg equilibrium. The 11 microsatellite markers developed in this study show polymorphic status. These markers are expected to be highly informative for further analysis of genetic diversity in N. cumingii.

Genetic relationships and diversity analysis in Turkish laurel (Laurus nobilis L.) germplasm using ISSR and SCoT markers.

Laurel (Laurus nobilis L.) has been used in the Mediterranean basin since ancient ages. Nowadays, Turkey, Mexico, Portugal, Italy, Spain, France, Algeria, and Morocco use aromatic leaves for commercial purposes, and Turkey is the largest exporter in the world. In this study, molecular characterization, and genetic relationships of 94 Turkish laurel genotypes were determined by ISSR and SCoT markers. The experiment was conducted with 16 ISSR and 10 SCoT markers. While 348 of 373 bands were polymorphic with a 93.3% polymorphism rate, Nei's genetic distances ranged between 0.17 and 0.70 with 0.39 mean in ISSR. In SCoT, 175 of 227 bands were polymorphic with 77.1% polymorphism rate, and Nei's genetic distances varied between 0.12 and 0.51. Sufficient genetic diversity determined with diversity parameters consisting of the average Shannon's information index (ISSR: 0.46, SCoT:0.35), the overall gene diversity (ISSR:0.19, SCoT:0.18), and the effective number of alleles (ISSR:1.52, SCoT:1.38). AMOVA (Analysis of molecular variance) revealed most of the variation was within genotypes (96%). Neighbor-joining algorithms, principal coordinate analysis (PCoA), and model-based structure resulted in harmony and clustered according to the geographical regions and provinces they collected. Genotypes were divided into two groups in ISSR and SCoT with UPGMA clustering resulting in a similar polymorphism distribution. The correlation coefficient (r) determined by marker systems' Nei's genetic distances was 0.25. The results of the study put forward resources for advanced breeding techniques, contribute to the preservation of genetic diversity, and management of genetic resources for the breeders.

Establishment of DNA fingerprints for Chrysosplenium using SRAP Markers

As a traditional Chinese medicinal material, Chrysosplenium is urgently needed for genetic resource investigation and protection research due to the decrease of its wild resources in recent years. After investigating the wild resources, we conducted genetic polymorphism and clustering studies of 24 species(a total of 36 samples) of Chrysosplenium using SRAP technique. The results showed that a total of 374 polymorphic bands were obtained using 18 pairs of SRAP primers to amplify these samples, on average of 20.7 bands for each primer pair. We used the biological software to analyze the population's genetic parameter and got the N_a value as 2.000 0, N_(e )value as 1.408 4, the average Nei's index as 0.263 5, and the average Shannon information index as 0.419 1. UPGMA cluster analysis showed that all the samples can be divided into three major groups at the genetic similarity coefficient of 0.70: there are 18 species(24 samples) gathered for the Ⅰ groups, 3 species or variation(7 samples) for Ⅱ groups, and 3 species(5 samples) for Ⅲ groups. The differences of these Chrysosplenium species at the molecular level are consistent with that of their geographical and ecological distribution. At the same time, we used SRAP technology to construct 36 DNA digital fingerprints of Chrysosplenium and obtained the unique molecular identification band type of each material. These results will provide effective methods and reliable basis for the identification, protection and genetic diversity analysis of the germplasm resources of Chrysosplenium, and lay a foundation for the further development and utilization of them.

Genomewide identification and development of microsatellite markers for Marssonina brunnea and their applications in two populations

SummaryMarssonina brunnea is an important pathogen that causes Marssonina leaf spot disease of poplar (MLDP) in various poplar species. Resistance breeding is considered as the main method for preventing this disease and requires information on genetic diversity and population structure. However, molecular markers that may be utilized in the identification of this fungus are limited. This study investigated the distribution of microsatellites in the M. brunnea genome. A total of 15,356 microsatellite markers (excluding mononucleotide repeats) were isolated from 50.1 Mb of genomic sequence. Eight M. brunnea isolates were evaluated in terms of 102 loci, followed by the selection of markers that could be utilized in investigating the population structure of 47 M. brunnea isolates from two populations. Twenty‐four polymorphic microsatellite markers were developed for M. brunnea. The number of alleles per locus ranged from two to eight (average: 3.75). The polymorphism information content (PIC) of these loci ranged from 0.0408 to 0.6492. The average Shannon's information index of these loci in the two populations was 0.3819 and 0.5351, respectively. Using these markers, M. brunnea isolates were mainly divided into two distinct clusters based on the relatedness of the sampling sites. These results indicate that the selected markers could be effectively utilized in investigating the population genetic structure of M. brunnea. This is the first report on microsatellite markers in M. brunnea.

Natural variation of selenium concentration in diverse tea plant (Camellia sinensis) accessions at seedling stage

Selenium (Se) is a dietary essential trace element for humans and animals. Owing to Se being obtained from food or other source of supplementation, Se-enriched tea is a possible source of supplemental Se and thus has been drawing much attention. This study aimed to identify the variation of the Se concentrations among 14 elite Camellia sinensis cultivars against two-Se-levels supplementation at seedling stage. In the present study, the genetic diversity was assessed by 93 alleles revealed by 12 SSR primers in the C. sinensis accessions. Among the scored 93 alleles, 81 (87.10%) were polymorphic, and the average Nei's gene diversity (He) was 0.253 and average shannon information index (I) was 0.394, indicating a relatively high genetic variation. Significant variations were observed for the Se concentration among the accessions in both treatments (P<0.01), ranging from 0.300–0.445mgkg−1 and 0.357–0.537mgkg−1 in control (0) and Se-supplied (4mgkg−1) treatments respectively. The quality components content, tea polyphenols and amino acid, were sensitive to Se-supplement in a few of accessions, whereas soluble sugar and aqueous extract content appeared unchanged between the contrast treatments. In addition, the genetic variation among the tea plant cultivars was not well correlated with the Se concentration. Even then, the genetic variation in Se concentration across the 14 accessions indicated the possibility of utilizing tea plant accessions to develop optimized cultivars for Se-enriched tea. For the relative high Se concentration in the tea, tea plant is supposed to be a Se-enriched species. These results may enhance our understanding the genetic variation in tea plant.

Genetic differentiation and diversity of Callosobruchus chinensis collections from China.

Callosobruchus chinensis (Linnaeus) is one of the most destructive pests of leguminous seeds. Genetic differentiation and diversity analysis of 345 C. chinensis individuals from 23 geographic populations using 20 polymorphic simple sequence repeats revealed a total of 149 alleles with an average of 7.45 alleles per locus. The average Shannon's information index was 1.015. The gene flow and genetic differentiation rate values at the 20 loci ranged from 0.201 to 1.841 and 11.0-47.2%, with averages of 0.849 and 24.4%, respectively. In the 23 geographic populations, the effective number of alleles and observed heterozygosity ranged from 1.441 to 2.218 and 0.191-0.410, respectively. Shannon's information index ranged from 0.357 to 0.949, with the highest value in Hohhot and the lowest in Rudong. In all comparisons, the fixation index (F ST ) values ranged from 0.049 to 0.441 with a total F ST value of 0.254 among the 23 C. chinensis populations, indicating a moderate level of genetic differentiation and gene flow among these populations. Analysis of molecular variance revealed that the genetic variation within populations accounted for 76.7% of the total genetic variation. The genetic similarity values between populations varied from 0.617 to 0.969, whereas genetic distances varied from 0.032 to 0.483. Using unweighted pair-group method using arithmetical averages cluster analysis, the 23 geographic collections were classified into four distinct genetic groups but most of them were clustered into a single group. The pattern of the three concentrated groups from polymerase chain reactions analysis showed a somewhat different result with cluster.

Genetic diversity in upland rice of Assam assessed through SSR markers

The genetic diversity in 100 upland rice germplasm of Assam, was analyzed using 120 SSR markers, of which 98 (81.66%) showed useful polymorphism with a total of 183 alleles. The number of alleles ranged from one to three with an average value of 1.867 per locus. The markers showed an average effective number of alleles to be 1.73, average Nei's gene diversity was 0.393, and average Shannon's Information Index was 0.556. The effective number of alleles and Shannon's information index showed positive correlation with the observed number of alleles. The resolving power of the 98 SSR primers ranged from 0.72 for primer RM38 to 2.82 for primer RM592. SSR generated an average similarity of 0.460 with similarity ranging from 0.07 to 1.00. Sufficient diversity was detected among the accessions. A basic molecular database was created for upland rice genotypes, which will be useful to identify and map useful genes that are harbored by these germplasms.

Genetic Diversity of Rice Landraces from Lowland and Upland Accessions of China

Genetic diversity of rice landraces from lowland and upland accessions of China was investigated using 66 polymorphic simple sequence repeat (SSR) markers. The total number of alleles detected from all 324 tested accessions was 555 with an average allele number (Na) of 8.409 per locus, the average effective number of alleles (Ne) of 3.574 and the average Shannon's information index (I) of 1.378. The genetic diversity was higher for the indica landraces compared to the japonica landraces, and the upland landraces were more genetically diverse than the lowland landraces. The SSR markers, RM72, RM232, RM219, RM241, RM224 and RM3 showed the highest rates of polymorphism and these SSR markers were suitable to assess the genetic diversity of rice germplasm resources. A dendrogram of 324 accessions of lowland and upland landraces showed that all rice accessions were mainly subdivided into two groups, japonica and indica, with some being intermediate. The distribution of lowland and upland landraces among the japonica and indica rice groups was distinct, with obvious differentiation between the lowland and upland landraces in japonica rice, but no such clear distinction in indica rice.

Population genetics of wild Hizikia fusiformis (Sargassaceae, Phaeophyta) along China’s coast

Hizikia fusiformis is one of the important commercially cultivated seaweeds in China. Inter-simple sequence repeats (ISSR) and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic structure of nine wild H. fusiformis populations collected along the coast of China. Of the 255 bands generated by 21 ISSR primers, 99.61% were polymorphic and 99.71% of 344 bands amplified by 30 SRAP primers were polymorphic. The tested high genetic diversities show that the average Nei's genetic diversity (H) were 0.1519 and 0.1624, and average Shannon's information index (I) were 0.2248 and 0.2400 in ISSR and SRAP analyses, respectively. Unweighted pair group method with arithmetic mean (UPGMA) dendrograms of the nine populations were divided into two main groups. The ISSR and SRAP analyses values of gene differentiation (G (ST), 0.5955, 0.5486, respectively) indicate that high variation exists among the nine populations, likely due to external interferences and limitation of gene flow (N (m) = 0.3397, 0.4114). Our study indicated that human activities and herbivore overgrazing had influenced the natural Hizikia populations and that the understanding of population genetics would be helpful in sustainable utilization and biomass conservation of Sargassaceae resources.

ISSR-based genetic diversity of Jatropha curcas germplasm in China

Jatropha curcas (Jatropha) is an oil-producing plant with multiple uses, especially the great potential of energy application. Germplasm collection and evaluation are essential for breeding new cultivars with high yield, good quality and wide adaptation. In the present study, we investigated genetic diversity of Chinese Jatropha germplasm by using ISSR markers. A set of 224 accessions including 219 from all the adaptation areas in China and five from Myanmar was adopted. Out of 100 UBC ISSR primers, 15 that had good reproducibility were selected to genotype the population. Among the 169 amplified bands, 127 (75.15%) were polymorphic which meant that Chinese Jatropha had high genetic diversity. Population genetics analysis showed that average Nei’s gene diversity ( He) was 0.19, and average Shannon Information Index ( I) was 0.292, indicating a relatively high genetic variation in the collections. The dendrogram based on Nei’s genetic distance showed that distinct genetic differentiation occurred in Chinese Jatropha, most of the mainland accessions were clustered into a sub-group (Ia), and accessions from Hainan Island and its neighboring Guangdong province were generally clustered into another sub-group (Ib). A core germplasm collection was established by SCR strategy. This core collection consisted of 46 accessions that accounted 20.54% of the initial collection, and maintained over 90% of observed alleles, polymorphic loci and polymorphism rate. Slight correlation of oil content variation and genetic diversity was observed. Tropical populations are the most important genetic resources and crosses between this tropics and the mainland are recommended for genetic improvement of Jatropha in China.

Genetic diversity analysis of Vitex trifolia var. simplicifolia populationswith inter-simple sequence repeats (ISSR) technique

To investigate 4 populations of 80 samples of Vitex trifolia var. simplicifolia collected from Shandong and Jiangxi province and analyze their intraspecies genetic variance. Inter-simple sequence repeat (ISSR) technique was applied for the study. Fifteen specific and stable primers were selected from 100 primers. A total of 129 sites were generated, and 115 of them (89.15%) were polymorphic. The data analyzed by PopGene demonstrated that the average polymorphic site percentage among the four populations was 71.89%. The average Shannon's information index was 0. 220 4. According to cluster analysis and the law of geographic variation, the populations were classified into two large groups: the Shandong group and the Jiangxi group. These results will provide the information for protection and utilization of V. trifolia var. simplicifolia and also further data for the study of genetic variation and species differentiation of V. trifolia var. simplicifolia.